tbuckley/cabot-search huggingface dataset:
Influenza Activity and Composition of the 2022–23 Influenza Vaccine — United States, 2021–22 Season
Authors: Angiezel Merced-Morales, Peter Daly, Anwar Isa Abd Elal, Noreen Ajayi, Ekow Annan, Alicia Budd, John Barnes, Arielle Colon, Charisse N. Cummings, A. Danielle Iuliano, Juliana DaSilva, Nick Dempster, Shikha Garg, Larisa Gubareva, Daneisha Hawkins, Amanda Howa, Stacy Huang, Marie Kirby, Krista Kniss, Rebecca Kondor, Jimma Liddell, Shunte Moon, Ha T. Nguyen, Alissa O’Halloran, Catherine Smith, Thomas Stark, Katie Tastad, Dawud Ujamaa, Dave E. Wentworth, Alicia M. Fry, Vivien G. Dugan, Lynnette Brammer
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Before the emergence of SARS-CoV-2, the virus that causes COVID-19, influenza activity in the United States typically began to increase in the fall and peaked in February. During the 2021-22 season, influenza activity began to increase in November and remained elevated until mid-June, featuring two distinct waves, with A(H3N2) viruses predominating for the entire season. This report summarizes influenza activity during October 3, 2021-June 11, 2022, in the United States and describes the composition of the Northern Hemisphere 2022-23 influenza vaccine. Although influenza activity is decreasing and circulation during summer is typically low, remaining vigilant for influenza infections, performing testing for seasonal influenza viruses, and monitoring for novel influenza A virus infections are important. An outbreak of highly pathogenic avian influenza A(H5N1) is ongoing; health care providers and persons with exposure to sick or infected birds should remain vigilant for onset of symptoms consistent with influenza. Receiving a seasonal influenza vaccine each year remains the best way to protect against seasonal influenza and its potentially severe consequences.
Hepatocyte β‐catenin loss is compensated by Insulin‐mTORC1 activation to promote liver regeneration
Authors: Shikai Hu, Catherine Cao, Minakshi Poddar, Evan Delgado, Sucha Singh, Anya Singh‐Varma, Donna Beer Stolz, Aaron Bell, Satdarshan P. Monga
Journal: Hepatology (2022)

Background and Aims: Liver regeneration (LR) following partial hepatectomy (PH) occurs via activation of various signaling pathways. Disruption of a single pathway can be compensated by activation of another pathway to continue LR. The Wnt–β‐catenin pathway is activated early during LR and conditional hepatocyte loss of β‐catenin delays LR. Here, we study mechanism of LR in the absence of hepatocyte‐β‐catenin. Approach and Results: Eight‐week‐old hepatocyte‐specific Ctnnb1 knockout mice (β‐catenin ΔHC ) were subjected to PH. These animals exhibited decreased hepatocyte proliferation at 40–120 h and decreased cumulative 14‐day BrdU labeling of &lt;40%, but all mice survived, suggesting compensation. Insulin‐mediated mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) activation was uniquely identified in the β‐catenin ΔHC mice at 72–96 h after PH. Deletion of hepatocyte regulatory‐associated protein of mTOR (Raptor), a critical mTORC1 partner, in the β‐catenin ΔHC mice led to progressive hepatic injury and mortality by 30 dys. PH on early stage nonmorbid Raptor ΔHC ‐β‐catenin ΔHC mice led to lethality by 12 h. Raptor ΔHC mice showed progressive hepatic injury and spontaneous LR with β‐catenin activation but died by 40 days. PH on early stage nonmorbid Raptor ΔHC mice was lethal by 48 h. Temporal inhibition of insulin receptor and mTORC1 in β‐catenin ΔHC or controls after PH was achieved by administration of linsitinib at 48 h or rapamycin at 60 h post‐PH and completely prevented LR leading to lethality by 12–14 days. Conclusions: Insulin‐mTORC1 activation compensates for β‐catenin loss to enable LR after PH. mTORC1 signaling in hepatocytes itself is critical to both homeostasis and LR and is only partially compensated by β‐catenin activation. Dual inhibition of β‐catenin and mTOR may have notable untoward hepatotoxic side effects.
Duodenoscope contamination and decontamination: more questions than answers
Authors: Klaus Mönkemüller
Journal: Endoscopy (2022)

Humans are populated by trillions of bacteria with their ratio to human cells being about 10:1 [1]. Whereas most bacteria, fungi, and viruses in humans live in perfect harmony and synergy, a few microorganisms may turn pathogenic if immunological or physical barrier disruption due to disease ensues. In addition, microbes may be introduced by external means, such as endoscopic procedures.
Prospective, multi-site study of patient outcomes after implementation of the TREWS machine learning-based early warning system for sepsis
Authors: Roy Adams, Katharine E. Henry, Anirudh Sridharan, Hossein Soleimani, Andong Zhan, Nishi Rawat, Lauren Johnson, David N. Hager, Sara E. Cosgrove, Andrew Markowski, Eili Y. Klein, Edward S. Chen, Mustapha O. Saheed, Maureen Henley, Sheila Miranda, Katrina Houston, Robert C. Linton, Anushree R. Ahluwalia, Albert W. Wu, Suchi Saria
Journal: Nature Medicine (2022)
Risk of residual neoplasia after a noncurative colorectal endoscopic submucosal dissection for malignant lesions: a multinational study
Authors: João Santos-Antunes, Mathieu Pioche, Felipe Ramos-Zabala, Paolo Cecinato, Francisco J. Gallego Rojo, Pedro Barreiro, Catarina Félix, Sandro Sferrazza, Frieder Berr, Andrej Wagner, Arnaud Lemmers, Mariana Figueiredo Ferreira, Eduardo Albéniz, Hugo Uchima, Ricardo Küttner-Magalhães, Carlos Fernandes, Rui Morais, Sunil Gupta, Daniel Martinho-Dias, Elisabete Rios, Isabel Faria-Ramos, Margarida Marques, Michael J. Bourke, Guilherme Macedo
Journal: Endoscopy (2022)

BACKGROUND : Endoscopic submucosal dissection (ESD) in colorectal lesions is technically demanding and a significant rate of noncurative procedures is expected. We aimed to assess the rate of residual lesions after a noncurative ESD for colorectal cancer (CRC) and to establish predictive scores to be applied in the clinical setting. METHODS : Retrospective multicenter analysis of consecutive colorectal ESDs. Patients with noncurative ESDs performed for the treatment of CRC lesions submitted to complementary surgery or with at least one follow-up endoscopy were included. RESULTS : From 2255 colorectal ESDs, 381 (17 %) were noncurative, and 135 of these were performed in CRC lesions. A residual lesion was observed in 24 patients (18 %). Surgery was performed in 96 patients and 76 (79 %) had no residual lesion in the colorectal wall or in the lymph nodes. The residual lesion rate for sm1 cancers was 0 %, and for > sm1 cancers was also 0 % if no other risk factors were present. Independent risk factors for lymph node metastasis were poor differentiation and lymphatic permeation (NC-Lymph score). Risk factors for the presence of a residual lesion in the wall were piecemeal resection, poor differentiation, and positive/indeterminate vertical margin (NC-Wall score). CONCLUSIONS : Lymphatic permeation or poor differentiation warrant surgery owing to their high risk of lymph node metastasis, mainly in > sm1 cancers. In the remaining cases, en bloc and R0 resections resulted in a low risk of residual lesions in the wall. Our scores can be a useful tool for the management of patients who undergo noncurative colorectal ESDs.
Underwater endoscopic mucosal resection for the diagnosis of metastatic gastric cancer in the descending colon
Authors: Satoki Shichijo, Hisashi Hara, Noriya Uedo, Tomoki Michida, Yoji Takeuchi
Journal: Endoscopy (2022)

A 55-year-old woman underwent total gastrectomy for advanced type 4 (nonulcerated, diffusely infiltrating) gastric cancer (pT4a) with negative margins and received adjuvant chemotherapy for 1 year. Three years later, she developed abdominal pain, and colonoscopy revealed stenosis on the left side of the colon. Biopsy evaluations showed no primary or metastatic tumor, and she was referred to our institution for further investigation and treatment. Computed tomography showed abnormal thickness of the colonic wall in the descending colon ([Fig. 1]). Colonoscopy revealed stenosis at the splenic flexure, and the colonoscope could not pass through ([Fig. 2]). Uneven ridges continued in the longitudinal direction on one side. Narrow-band imaging showed no apparent tumor on the mucosa ([Fig. 3]). Endoscopically, we diagnosed metastatic gastric cancer or primary advanced type 4 colonic cancer.
Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis
Authors: Laurel Romano, Katie G. Seu, Julien Papoin, David E. Muench, Diamantis Konstantinidis, André Olsson, Katrina Schlum, Kashish Chetal, Joel Anne Chasis, Narla Mohandas, Betsy J. Barnes, Yi Zheng, H. Leighton Grimes, Nathan Salomonis, Lionel Blanc, Theodosia A. Kalfa
Journal: Blood (2022)
Spasmodic contraction induced by high concentration iodine staining to facilitate underwater endoscopic mucosal resection of early esophageal cancer
Authors: Chao Deng, Suhua Wu, Feng Xu, Li Zhong, Ying Huang, Zhechuan Mei, Song He
Journal: Endoscopy (2022)

A 61-year-old man was diagnosed with early esophageal cancer by endoscopy and pathological biopsy. The lesion of about 1 cm in diameter met the indications for endoscopic resection after preoperative evaluation. The markers around the lateral margin of cancer were made by the snare tip with soft coagulation (Effect 5, 80 W) ([Fig. 1 a]).
Factors driving provider adoption of the TREWS machine learning-based early warning system and its effects on sepsis treatment timing
Authors: Katharine E. Henry, Roy Adams, Cassandra Parent, Hossein Soleimani, Anirudh Sridharan, Lauren Johnson, David N. Hager, Sara E. Cosgrove, Andrew Markowski, Eili Y. Klein, Edward S. Chen, Mustapha O. Saheed, Maureen Henley, Sheila Miranda, Katrina Houston, Robert C. Linton, Anushree R. Ahluwalia, Albert W. Wu, Suchi Saria
Journal: Nature Medicine (2022)
Human–machine teaming is key to AI adoption: clinicians’ experiences with a deployed machine learning system
Authors: Katharine E. Henry, Rachel Kornfield, Anirudh Sridharan, Robert C. Linton, Catherine Groh, Tony Wang, Albert Wu, Bilge Mutlu, Suchi Saria
Journal: npj Digital Medicine (2022)

While a growing number of machine learning (ML) systems have been deployed in clinical settings with the promise of improving patient care, many have struggled to gain adoption and realize this promise. Based on a qualitative analysis of coded interviews with clinicians who use an ML-based system for sepsis, we found that, rather than viewing the system as a surrogate for their clinical judgment, clinicians perceived themselves as partnering with the technology. Our findings suggest that, even without a deep understanding of machine learning, clinicians can build trust with an ML system through experience, expert endorsement and validation, and systems designed to accommodate clinicians' autonomy and support them across their entire workflow.
New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread
Authors: Jiansi Gao, Michael R May, Bruce Rannala, Brian R Moore
Journal: Molecular Biology and Evolution (2022)

Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all such studies are based on phylodynamic models that assume-despite direct and compelling evidence to the contrary-that rates of viral geographic dispersal are constant through time. Here, we: (1) extend phylodynamic models to allow both the average and relative rates of viral dispersal to vary independently between pre-specified time intervals; (2) implement methods to infer the number and timing of viral dispersal events between areas; and (3) develop statistics to assess the absolute fit of discrete-geographic phylodynamic models to empirical datasets. We first validate our new methods using simulations, and then apply them to a SARS-CoV-2 dataset from the early phase of the COVID-19 pandemic. We show that: (1) under simulation, failure to accommodate interval-specific variation in the study data will severely bias parameter estimates; (2) in practice, our interval-specific discrete-geographic phylodynamic models can significantly improve the relative and absolute fit to empirical data; and (3) the increased realism of our interval-specific models provides qualitatively different inferences regarding key aspects of the COVID-19 pandemic-revealing significant temporal variation in global viral dispersal rates, viral dispersal routes, and the number of viral dispersal events between areas-and alters interpretations regarding the efficacy of intervention measures to mitigate the pandemic.
Pancreatic duct stenting using an endoscopic ultrasound-guided intrapancreatic duct rendezvous technique
Authors: Kazunari Nakahara, Yosuke Michikawa, Junya Sato, Yosuke Igarashi, Akihiro Sekine, Yusuke Satta, Keisuke Tateishi
Journal: Endoscopy (2022)

A patient was admitted for pancreatic stenting for pancreatic duct stricture due to chronic pancreatitis. However, transpapillary stenting failed because a guidewire could not pass the severe stricture in the pancreatic head. Therefore, endoscopic ultrasound-guided pancreatic duct drainage (EUS-PD) was conducted by puncture from the stomach, and a plastic stent was placed on the caudal side of the stricture [1] [2]. Following EUS-PD fistula creation, the pancreatic duct was cannulated through the fistula ([Fig. 1 a]), and the guidewire passed through the stricture and was placed in the duodenum via the minor papilla ([Fig. 1 b]). The endoscope was withdrawn leaving the guidewire in place, followed by duodenoscope insertion into the duodenum. Pancreatic duct cannulation and endoscopic pancreatic sphincterotomy were performed using a rendezvous technique [3]; however, the cannula and dilators could not pass the stricture. Therefore, we again switched to the procedure via the EUS-PD fistula, and a 7-Fr stent retriever allowed the breakthrough of the stricture [4] ([Fig. 2a]), followed by dilation of the stricture with a 6-mm balloon catheter ([Fig. 2b]). However, the plastic stent (7 Fr; SUZAKU, Kaneka Medics, Tokyo, Japan) could only be inserted to the midpoint of the stricture ([Fig. 3]). Therefore, the pancreatic duct was cannulated via the minor papilla, and the guidewire was inserted into the stent lumen ([Fig. 4]). Subsequently, a thin-tipped balloon catheter (4 mm; REN; Kaneka Medics) was inserted into the stent over the guidewire, and the balloon was inflated. Finally, the balloon catheter was pulled, and the stent was successfully placed across the minor papilla ([Fig. 5a,b]).
Prophylactic steroid use is ineffective in food allergy: A randomized‐controlled clinical trial and a murine model
Authors: Teruaki Matsui, Hirotaka Yamashita, Katsumasa Kitamura, Atsushi Makino, Yoshihiro Takasato, Shiro Sugiura, Komei Ito
Journal: Allergy (2022)

Appendix S1 Appendix S2 Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
How to confirm the appropriate incision depth using a guidewire during needle-knife fistulotomy
Authors: Tesshin Ban, Yoshimasa Kubota, Tomoaki Ando
Journal: Endoscopy (2022)

An early attempt at needle-knife fistulotomy (NKF) is the rescue technique for selective biliary cannulation (SBC) [1] [2] [3]. To complete NKF, it is crucial to identify critical landmarks, including the glistening pink adventitia of the bile duct, the onion skin-like biliary orifice within the incision, and the pearly-white biliary mucosa [4]. However, owing to the diversity of papillary morphology, it is challenging to identify these landmarks and determine appropriate incision depth in every individual attempt [5].
Herpes simplex virus lymphadenitis is associated with tumor reduction in a patient with chronic lymphocytic leukemia
Authors: Andres Chang, Anton M. Sholukh, Andreas Wieland, David L. Jaye, Mary Carrington, Meei-Li Huang, Hong Xie, Keith R. Jerome, Pavitra Roychoudhury, Alexander L. Greninger, Jean L. Koff, Jonathon B. Cohen, David M. Koelle, Lawrence Corey, Christopher R. Flowers, Rafi Ahmed
Journal: Journal of Clinical Investigation (2022)

BackgroundHerpes simplex virus lymphadenitis (HSVL) is an unusual presentation of HSV reactivation in patients with chronic lymphocytic leukemia (CLL) and is characterized by systemic symptoms and no herpetic lesions. The immune responses during HSVL have not, to our knowledge, been studied.MethodsPeripheral blood and lymph node (LN) samples were obtained from a patient with HSVL. HSV-2 viral load, antibody levels, B and T cell responses, cytokine levels, and tumor burden were measured.ResultsThe patient showed HSV-2 viremia for at least 6 weeks. During this period, she had a robust HSV-specific antibody response with neutralizing and antibody-dependent cellular phagocytotic activity. Activated (HLA-DR+, CD38+) CD4+ and CD8+ T cells increased 18-fold, and HSV-specific CD8+ T cells in the blood were detected at higher numbers. HSV-specific B and T cell responses were also detected in the LN. Markedly elevated levels of proinflammatory cytokines in the blood were also observed. Surprisingly, a sustained decrease in CLL tumor burden without CLL-directed therapy was observed with this and also a prior episode of HSVL.ConclusionHSVL should be considered part of the differential diagnosis in patients with CLL who present with signs and symptoms of aggressive lymphoma transformation. An interesting finding was the sustained tumor control after 2 episodes of HSVL in this patient. A possible explanation for the reduction in tumor burden may be that the HSV-specific response served as an adjuvant for the activation of tumor-specific or bystander T cells. Studies in additional patients with CLL are needed to confirm and extend these findings.FundingNIH grants 4T32CA160040, UL1TR002378, and 5U19AI057266 and NIH contracts 75N93019C00063 and HHSN261200800001E. Neil W. and William S. Elkin Fellowship (Winship Cancer Institute).
Endoscopic management of cystic duct stumpitis
Authors: Monica Passi, Petros C. Benias, Arvind J. Trindade
Journal: Endoscopy (2022)

A 62-year-old man who underwent an uncomplicated laparoscopic cholecystectomy 1 year prior for acute gangrenous cholecystitis presented with abdominal pain. Computed tomography demonstrated a dilated cystic duct remnant with stones ([Fig. 1]), confirmed on magnetic resonance cholangiopancreatography. The patient declined surgical intervention. Given the recent evidence [1], the patient was referred for an endoscopic retrograde cholangiopancreatography (ERCP).
Letter to the editor: Reflection on the no‐association between the presence of fatty liver disease and mortality in the elderly
Authors: Cong Ning, Shi‐Tao Jiang, Xin‐Ting Sang
Journal: Hepatology (2022)

To the editor, We followed with interest the report by Laurens et al. on increased mortality that was not associated with fatty liver disease (FLD) in the elderly.1 Their impressive results suggested that screening for hepatic steatosis in the elderly was unlikely to improve outcome, which was different from the recommendations of several current guidelines. However, the findings should be interpreted with caution given the following aspects. First, in this study, 8.0 kPa was used as the threshold for categorizing liver stiffness (LS). Previous studies have shown that patients with cirrhosis typically have an LS of >12–15 kPa.2 Choosing different thresholds may lead to entirely different conclusions. How to determine a reasonable cut‐off value needs further explanation. In addition, the prevalence of advanced fibrosis in patients with NAFLD >60 years old is higher than in younger patients, which is related to slow development of the natural history of NAFLD.3 However, all‐cause and liver‐related mortality of patients with stage 4 fibrosis are higher than those without fibrosis.4 Monitoring and intervention of liver fibrosis (LF) in elderly patients with FLD may improve the survival of this population. To our knowledge, NAFLD has a solid genetic background. Some studies have shown that Asians have a higher mortality rate than Europeans with the same level of obesity.5 The study suggests that populations of different races may have different degrees of susceptibility to NAFLD, leading to heterogeneity in clinical outcomes. Considering that the characteristics of NAFLD may differ substantially between ethnic groups, we believe that it is necessary to validate the findings of this study in a prospective cohort that includes different ethnicities. Third, this cohort study is susceptible to detection and selection bias because patients with FLD may be subject to more medical monitoring and lifestyle supervision (e.g., exercise and coffee consumption) after the initial diagnosis. The improvement of baseline characteristics and adjustment during model fitting will improve the evidence level of research results. In conclusion, this study provides a new reference for developing FLD and LF screening programs in the elderly.
A novel case of biliary common bile duct reconstruction by the rendezvous technique using endoscopic cholangioscopy and percutaneous cholangioscopy
Authors: Jean-Philippe Ratone, Fabrice Caillol, Mariola Marx, Solene Hoibian, Yanis Dahel, Marc Giovannini, Jacques Devière
Journal: Endoscopy (2022)

Biliary tract injuries during cholecystectomy are a rare, but not exceptional, adverse event, with severe consequences. The Strasberg classification with Bismuth modification is most frequently used to classify biliary tract injuries [1] [2]. Expertise in endoscopic, radiologic, and surgical management is required, especially for major biliary tract injuries [3]. A transhepatic-endoscopic approach is useful in difficult cases [4] [5]. We aim to describe a new solution after failure of the standard rendezvous technique, namely double cholangioscopy rendezvous.
Intratumoral oncolytic herpes virus G47∆ for residual or recurrent glioblastoma: a phase 2 trial
Authors: Tomoki Todo, Hirotaka Ito, Yasushi Ino, Hiroshi Ohtsu, Yasunori Ota, Junji Shibahara, Minoru Tanaka
Journal: Nature Medicine (2022)

This investigator-initiated, phase 2, single-arm trial primarily assessed the efficacy of G47∆, a triple-mutated, third-generation oncolytic herpes simplex virus type 1, in 19 adult patients with residual or recurrent, supratentorial glioblastoma after radiation therapy and temozolomide (UMIN-CTR Clinical Trial Registry UMIN000015995). G47Δ was administered intratumorally and repeatedly for up to six doses. The primary endpoint of 1-yr survival rate after G47∆ initiation was 84.2% (95% confidence interval, 60.4-96.6; 16 of 19). The prespecified endpoint was met and the trial was terminated early. Regarding secondary endpoints, the median overall survival was 20.2 (16.8-23.6) months after G47∆ initiation and 28.8 (20.1-37.5) months from the initial surgery. The most common G47∆-related adverse event was fever (17 of 19) followed by vomiting, nausea, lymphocytopenia and leukopenia. On magnetic resonance imaging, enlargement of and contrast-enhancement clearing within the target lesion repeatedly occurred after each G47∆ administration, which was characteristic to this therapy. Thus, the best overall response in 2 yr was partial response in one patient and stable disease in 18 patients. Biopsies revealed increasing numbers of tumor-infiltrating CD4+/CD8+ lymphocytes and persistent low numbers of Foxp3+ cells. This study showed a survival benefit and good safety profile, which led to the approval of G47∆ as the first oncolytic virus product in Japan.